/*
 * Copyright (c) 2011 Seoul National University
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met: redistributions of source code must retain the above copyright
 * notice, this list of conditions and the following disclaimer;
 * redistributions in binary form must reproduce the above copyright
 * notice, this list of conditions and the following disclaimer in the
 * documentation and/or other materials provided with the distribution;
 * neither the name of the copyright holders nor the names of its
 * contributors may be used to endorse or promote products derived from
 * this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
 * Authors: Jung Ho Ahn  ( gajh@snu.ac.kr )
 *
 */

#ifndef __INPUTOPTIONS_H__
#define __INPUTOPTIONS_H__

#include <cstdint>
#include <iostream>
#include <list>
#include <map>
#include <string>


using namespace std;

class InputOptions
{
  public:
    InputOptions(const string & optionfile, bool is_cin_empty = true);
    ~InputOptions();
    
    map<string, string> params;
    list<string>        fasta_filenames;
    list<string>        fastq_filenames;
    
    uint64_t get_param_uint64(const string & str, uint64_t def) const;
    string   get_param_str(const string & str) const;
    bool     get_param_bool(const string & str, bool default_value = false) const;
};
 
#endif  // __INPUTOPTIONS_H__
